Merge branch 'documentation' into 'master'

Documentation

See merge request mass-spectrometry/corems!68

Author: corilo

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.5.3
+current_version = 2.0.0
 commit = False
 tag = False
 

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "2.5.3-1005"
+current_version = "2.0.0-1005"
 parse = '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<build>\d+))?'
 serialize = ["{major}.{minor}.{patch}-{build}",
             "{major}.{minor}.{patch}"]

.gitlab-ci.yml

@@ -95,7 +95,7 @@ build:
 #     KUBERNETES_CPU_LIMIT: "2"
 #     KUBERNETES_MEMORY_REQUEST: 2Gi
 #     KUBERNETES_MEMORY_LIMIT: 8Gi
-#     CONTAINER_TAG: "2.5.3-1005"
+#     CONTAINER_TAG: "2.0.0-1005"
 
 # deployment:
 

README.md

@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `2.5.3.beta`
+ `2.0`
 
 ## Main Developers/Contact 
 - [Yuri. E. Corilo](mailto:[email protected])  
@@ -104,11 +104,10 @@ CoreMS aims to provide
 - Peak picking using apex quadratic fitting
 - Experimental resolving power calculation
 - Frequency and m/z domain calibration functions:
-- LedFord equation [ref]
+- LedFord equation
 - Linear equation
 - Quadratic equation
 - Automatic search most abundant **Ox** homologue series
-- Step fit ('walking calibration") based on the LedFord equation [ref]
 - Automatic local (SQLite) or external (PostgreSQL) database check, generation, and search
 - Automatic molecular formulae assignments algorithm for ESI(-) MS for natural organic matter analysis
 - Automatic fine isotopic structure calculation and search for all isotopes
@@ -302,11 +301,11 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 ## Citing CoreMS
 
 If you use CoreMS in your work, please use the following citation:
-Version [1.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v1.0.0), archived on Zenodo:  
+Version [2.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v2.0.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641553.svg)](https://doi.org/10.5281/zenodo.4641553)
 ```
-Yuri E. Corilo, William R. Kew, Lee Ann McCue (2021, March 27). EMSL-Computing/CoreMS: CoreMS 1.0.0 (Version v1.0.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641553
+Yuri E. Corilo, William R. Kew, Lee Ann McCue (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.0 (Version v2.0.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641553
 ```
 ## Disclaimer
 

corems-k8s-debug.yaml

@@ -14,7 +14,7 @@ spec:
     spec:
       containers:
       - name: corems-debug-container
-        image: code-registry.emsl.pnl.gov/mass-spectrometry/corems/corems-base-310-dotnet6:2.5.3-1003
+        image: code-registry.emsl.pnl.gov/mass-spectrometry/corems/corems-base-310-dotnet6:2.0.0-1003
         command: ["/bin/sh"]  # Specify the shell as the command
         args: ["-c", "sleep infinity"]  # Run a command that keeps the container running
         stdin: true

corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = 'Yuri E. Corilo'
-__version__ = '2.5.3.beta'
+__version__ = '2.0.0'
 __doc__ = '''
 [![DOI](https://zenodo.org/badge/265072913.svg)](https://zenodo.org/badge/latestdoi/265072913)
 

corems/encapsulation/factory/parameters.py

@@ -73,6 +73,9 @@ class LCMSParameters:
 
 def default_parameters(file_location):  # pragma: no cover
     """Generate parameters dictionary with the default parameters for data processing
+       To gather parameters from instrument data during the data parsing step, a parameters dictionary with the default parameters needs to be generated.
+       This dictionary acts as a placeholder and is later used as an argument for all the class constructor methods during instantiation. 
+       The data gathered from the instrument is added to the class properties.
 
     Parameters
     ----------

corems/encapsulation/factory/processingSetting.py

@@ -16,7 +16,7 @@ class TransientSetting:
     implemented_apodization_function : tuple
         Available apodization functions
     apodization_method : str
-        Apodization function to use. Hanning is a good default. For absorption mode processing, Half-Sine or Half-Kaiser may be more appropriate.
+        Apodization function to use. Hanning is a good default for Fourier transform magnitude mode. For absorption mode processing, Half-Sine or Half-Kaiser may be more appropriate.
     number_of_truncations : int
         How many times to truncate the transient prior to Fourier transform
     number_of_zero_fills : int
@@ -120,15 +120,15 @@ class LiquidChromatographSetting:
     peak_max_prominence_percent : float, optional
         1-100 % used for baseline detection. Default is 1.
     peak_derivative_threshold : float, optional
-        Default is 0.0005.
+        Threshold for defining derivative crossing. Default is 0.0005.
     min_peak_datapoints : float, optional
-        Default is 5.
+        minimum data point to define a chromatografic peak. Default is 5.
     noise_threshold_method : str, optional
         Method for detecting noise threshold. Default is 'manual_relative_abundance'.
     noise_threshold_methods_implemented : tuple, optional
         Methods for detected noise threshold that can be implemented. Default is ('auto_relative_abundance', 'manual_relative_abundance', 'second_derivative').
     std_noise_threshold : int, optional
-        Default is 3.
+        the amount of standard deviations used to calculate noise thresould, average + (std_noise_threshold * noise). Default is 3.
     peak_height_min_percent : float, optional
         0-100 % used for peak detection. Default is 0.1.
     eic_signal_threshold : float, optional

corems/encapsulation/output/parameter_to_json.py

@@ -6,9 +6,17 @@
 from corems.encapsulation.output import parameter_to_dict 
 
 def dump_all_settings_json(filename='SettingsCoreMS.json', file_path=None):
+    """
+    Write JSON file into current directory with all the default settings for the CoreMS package.
+    
+    Parameters:
+    ----------
+    filename : str, optional
+        The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
+    file_path : str or Path, optional
+        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
+    """
 
-    '''Write JSON file into current directory
-    '''        
     data_dict_all = parameter_to_dict.get_dict_all_default_data()
 
     if not file_path:
@@ -24,17 +32,22 @@ def dump_all_settings_json(filename='SettingsCoreMS.json', file_path=None):
         outfile.write(output)
 
 def dump_ms_settings_json(filename='SettingsCoreMS.json', file_path=None):
-    
-    '''Write JSON file into current directory
-    '''        
-    data_dict = parameter_to_dict.get_dict_ms_default_data()
+    """
+    Write JSON file into current directory with all the mass spectrum default settings for the CoreMS package.
+
+    Parameters
+    ----------
+    filename : str, optional
+        The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
+    file_path : str or Path, optional
+        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
 
+    """
+    data_dict = parameter_to_dict.get_dict_ms_default_data()
     if not file_path:
-        
         file_path = Path.cwd() / filename 
 
     with open(file_path, 'w', encoding='utf8', ) as outfile:
-            
         import re
         #pretty print 
         output = json.dumps(data_dict, sort_keys=False, indent=4, separators=(',', ': '))
@@ -43,72 +56,98 @@ def dump_ms_settings_json(filename='SettingsCoreMS.json', file_path=None):
         outfile.write(output)
 
 def dump_gcms_settings_json(filename='SettingsCoreMS.json', file_path=None):
-    '''Write JSON file into current directory
-    '''        
+    """
+    Write JSON file into current directory containing the default GCMS settings data.
+
+    Parameters
+    ----------
+    filename : str, optional
+        The name of the JSON file to be created. Default is 'SettingsCoreMS.json'.
+    file_path : str or Path-like object, optional
+        The path where the JSON file will be saved. If not provided, the file will be saved in the current working directory.
+    """
+
     from pathlib import Path
     import json
 
     data_dict = parameter_to_dict.get_dict_gcms_default_data()
 
     if not file_path:
-        
         file_path = Path.cwd() / filename 
 
     with open(file_path, 'w', encoding='utf8', ) as outfile:
-            
         import re
         #pretty print 
         output = json.dumps(data_dict, sort_keys=False, indent=4, separators=(',', ': '))
         output = re.sub(r'",\s+', '", ', output)
 
-        outfile.write(output)       
+        outfile.write(output)
 
 def dump_all_settings_toml(filename='SettingsCoreMS.toml', file_path=None):
-    
+    """
+    Write TOML file into the specified file path or the current directory with all the default settings for the CoreMS package.
+
+    Parameters
+    ----------
+    filename : str, optional
+        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
+    file_path : str or Path, optional
+        The path where the TOML file will be saved. If not provided, the file will be saved in the current directory.
+
+    """
     from pathlib import Path
 
-    '''Write TOML file into current directory
-    '''        
     data_dict_all = parameter_to_dict.get_dict_all_default_data()
 
     if not file_path:
-        file_path = Path.cwd() / filename 
+        file_path = Path.cwd() / filename
 
     with open(file_path, 'w', encoding='utf8', ) as outfile:
-            
         import re
-        #pretty print 
         output = toml.dumps(data_dict_all)
         outfile.write(output)
 
 def dump_ms_settings_toml(filename='SettingsCoreMS.toml', file_path=None):
-    
-    '''Write TOML file into current directory
-    '''        
+    """
+    Write TOML file into the current directory with all the mass spectrum default settings for the CoreMS package.
+
+    Parameters
+    ----------
+    filename : str, optional
+        The name of the TOML file to be created. Default is 'SettingsCoreMS.toml'.
+    file_path : str or Path, optional
+        The path where the TOML file should be saved. If not provided, the file will be saved in the current working directory.
+
+    """
     data_dict = parameter_to_dict.get_dict_ms_default_data()
 
     if not file_path:
-        
         file_path = Path.cwd() / filename 
 
     with open(file_path, 'w', encoding='utf8', ) as outfile:
-            
         import re
-        #pretty print 
+        # pretty print 
         output = toml.dumps(data_dict)
         outfile.write(output)
 
 def dump_gcms_settings_toml(filename='SettingsCoreMS.toml', file_path=None):
-    '''Write TOML file into current directory
-    '''        
+    """
+    Write TOML file into current directory containing the default GCMS settings data.
+
+    Parameters
+    ----------
+    filename : str, optional
+        The name of the TOML file. Defaults to 'SettingsCoreMS.toml'.
+    file_path : str or Path, optional
+        The path where the TOML file will be saved. If not provided, the file will be saved in the current working directory.
     
+    """
+
     data_dict = parameter_to_dict.get_dict_gcms_default_data()
 
     if not file_path:
-        
         file_path = Path.cwd() / filename 
 
     with open(file_path, 'w', encoding='utf8', ) as outfile:
-            
         output = toml.dumps(data_dict)
-        outfile.write(output)               
+        outfile.write(output)